Primers for isothermal amplification of hepatitis C virus

ABSTRACT

The present application relates to primers for isothermal amplification of HCV each include at least eighteen consecutive bases corresponding to a 3′ end region of one selected from base sequences of SEQ ID NOs: 1-10, 21 and 22. The primers are specific to HCV subtypes  1   a,    1   b,    2   a,    2   b  and  3   a , respectively and enable genotyping of HCV by isothermal amplification.

CLAIM OF PRIORITY

The present application claims priority from Japanese application JP 2004-149448 filed on May 19, 2004, the content of which is hereby incorporated by reference into this application.

FIELD OF THE INVENTION

The present invention relates to primers for isothermal amplification of subtypes of hepatitis C virus (hereinafter briefly referred to as “HCV”), and methods for detecting or determining HCV using the primers.

BACKGROUND OF THE INVENTION

Chiron Corporation, Emeryville, Calif. identified the gene of HCV in 1988. The genome sequence of HCV including about 9,500 bases has been identified, and it has been revealed that HCV has a single strand RNA as its genome. HCV is often accompanied with mutation in its gene sequence, is classified as four to six subgroups based on gene sequences in regions accompanied with frequent mutation, and is further classified as, for example, subtypes 1 a, 1 b, 2 a, 2 b and 3 a (P. Simmonds, et al., J. Gen Virol., 74, 661-668 (1993))

Only two- to three-tenths of subjects infected with HCV have subjective symptoms such as malaise, and most of them undergo chronic inflammation without subjective symptoms and may further undergo liver cirrhosis and liver cancer. It is difficult to detect HCV at initial stage of HCV infection by immunoassay using antibodies and to prevent the symptoms from becoming worse and/or the infected blood completely from contaminating into blood for transfusion.

Recent years, however, have seen significant advances as a result of intensive studies and have enabled the detection of HCV infection and genotyping of HCV even at initial stage of HCV infection by a genetic test in which a gene is amplified. The genotyping enables determination of the incidence rate of acute hepatitis, the rate of becoming chronic and the possibility of shifting from hepatitis via liver cirrhosis to liver cancer, enables the prediction of efficacies of administration of an interferon selected depending on the subtype and enables the identification of contagion sources and infection route. Thus, the detection or determination of HCV by such a genetic test becomes superior to immunoassay.

Certain methods for genotyping HCV have been reported. Okamoto et al., for example, have reported a method for genotyping HCV, including the steps of preparing seven different primers using a core region of HCV as a target, and carrying out a reverse transcription polymerase chain reaction (RT-PCR) using a reverse transcriptase in combination with a suitable set of primers in J. Gen. Virol., 73, 673-679 (1992). A certain method for genotyping HCV in its NS5-region has been reported. Japanese Patent Application Laid-Open (JP-A) No. 09-75100 and F. McOmish, et al. in Transfusion, 33, 7-13 (1993) have reported a method including the steps of cleaving an amplified product of the 5′-untranslated region of HCV with a restriction enzyme and then genotyping HCV. Other methods for genotyping have been reported, including the steps of directly sequencing the amplified product just mentioned above, and genotyping HCV based on the resulting base sequence information [Germer J. J., et al., J. Clin. MiCrobiol., 37(8), 2625-2630 (1999); Holland J., et al., Pathology, 30(2), 192-195 (1998); and Doglio A., et al., Res. Virol., 149(4), 219-227 (1998)].

All the conventional oligonucleotide primers for genotyping HCV are to be amplified by PCR, and no oligonucleotide primer for genotyping HCV by isothermal amplification has been reported. This is probably because the HCV RNA has a complicated secondary structure as a result typically of intramolecular hydrogen bonds, a region that can be amplified by isothermal amplification is restricted, and it is very difficult to design specific primers capable of carrying out genotyping in the region. A method for quantitatively determining HCV by nucleic acid sequence-based amplification (NASBA), a kind of isothermal amplification, has been reported (Guichon A., et al., J. Clin. Virol., 29, 84-91 (2004)). This technique cannot determine the genotype of HCV gene although it can amplify the HCV gene. Specifically, all the conventional HCV genotyping techniques using oligonucleotide primers require complicated temperature control in PCR and invite complicated procedures, long time and high cost for the determination and are not satisfactory. Demands have therefore been made to develop oligonucleotide primers that enable genotyping of HCV by isothermal amplification.

SUMMARY OF THE INVENTION

Accordingly, an object of the present invention is to provide a technique for genotyping HCV by isothermal amplification. Another object of the present invention is to provide primers specific to HCV subtypes 1 a, 1 b, 2 a, 2 b and 3 a for use in the technique.

The present inventors have successfully designed primers that enable genotype-specific isothermal amplification in a core region of gene sequences belonging to HCV subtypes 1 a, 1 b, 2 a, 2 b and 3 a genes. The isothermal amplification of a HCV sample using these primers results in genotype-specific amplification and thereby enables detection and genotyping of HCV subtypes 1 a, 1 b, 2 a, 2 b and 3 a genes based on whether or not amplification occurs.

Specifically, the present invention provides, in an aspect, a primer for isothermal amplification of HCV, comprising at least eighteen consecutive bases corresponding to a 3′ end region of one base sequence selected from the group consisting of SEQ ID NOs: 1-10, 21 and 22.

The primer can further include a T7 promoter sequence in its 5′-end region typically when used in NASBA.

The present invention further provides, in another aspect, a pair of primers for isothermal amplification of hepatitis C virus, selected from the following pairs of primers (1) to (5):

(1) a pair of primers comprising at least eighteen consecutive bases corresponding to a 3′ end region of the base sequences of SEQ ID NOs: 1 and 2, respectively;

(2) a pair of primers comprising at least eighteen consecutive bases corresponding to a 3′ end region of the base sequences of SEQ ID NOs: 3 and 4, respectively, or a pair of primers comprising at least eighteen consecutive bases corresponding to a 3′ end region of the base sequences of SEQ ID NOs: 3 and 9, respectively;

(3) a pair of primers comprising at least eighteen consecutive bases corresponding to a 3′ end region of the base sequences of SEQ ID NOs: 5 and 6, respectively, or a pair of primers comprising at least eighteen consecutive bases corresponding to a 3′ end region of the base sequences of SEQ ID NOs: 5 and 10, respectively;

(4) a pair of primers comprising at least eighteen consecutive bases corresponding to a 3′ end region of the base sequences of SEQ ID NOs: 7 and 8, respectively; and

(5) a pair of primers comprising at least eighteen consecutive bases corresponding to a 3′ end region of the base sequences of SEQ ID NOs: 21 and 22, respectively.

When used typically in NASBA, at least one of the pair of primers can further include a T7 promoter sequence in its 5′-end region.

The present invention further provides, in yet another aspect, a method for detecting HCV, including the steps of subjecting a clinical sample to isothermal amplification with at least one of the pairs of primers according to the present invention, and determining a HCV subtype based on the resulting amplified product.

The method for detecting HCV enables determination of a HCV subtype. When isothermal amplification is carried out by NASBA, at least one of the pair of primers can further include a T7 promoter sequence.

The detection method of the present invention can simultaneously detect two or more HCV subtypes by using two or more pairs of primers of the present invention.

In addition and advantageously, the present invention provides a kit for use in the method for detecting HCV. The kit essentially includes at least one pair of primers of the present invention, and at least one probe containing a sequence complementary to an amplified product amplified by the action of the at least one pair of primers and serving to detect the amplified product and may further include, as needed, any of components that can be used in gene amplification and determination of amplified products, such as molecular weight markers, enzymes, dNTPs, NTPs and sterilized water, as well as any other components.

The primers of the present invention enable the detection and genotyping of a HCV subtype by isothermal amplification. The present invention therefore enables easy and rapid detection (determination) and genotyping of HCV without requiring complicated temperature control as in PCR.

Further objects, features and advantages of the present invention will become apparent from the following description of the preferred embodiments with reference to the attached drawings.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a flow chart of HCV genotyping;

FIG. 2 is a flow chart of amplification by NASBA;

FIG. 3 shows an electropherogram obtained by genotyping of HCV samples using oligonucleotide primers of the present invention;

FIG. 4 is a flow chart of real-time genotyping of HCV gene;

FIGS. 5A and 5B illustrate real-time genotyping of HCV using oligonucleotide primers according to the present invention using a HCV RNA of subtype 1 b and a HCV RNA of subtype 2 a as a sample, respectively;

FIG. 6 shows an electropherogram obtained by genotyping of HCV subtypes 1 b and 2 b using oligonucleotide primers of the present invention;

FIG. 7 shows an electropherogram obtained by the amplification of a HCV subtype 1 a sample using oligonucleotide primers according to the present invention;

FIG. 8 shows an electropherogram obtained by the amplification of HCV subtype 1 b sample using oligonucleotide primers of SEQ ID NOs: 1 and 11; and

FIG. 9 schematically illustrates the configuration of primers for isothermal amplification selective to the HCV subtype 1 a gene.

DESCRIPTION OF THE PREFERRED EMBODMIENTS

1. Primers for Isothermal Amplification of HCV

The present inventors have designed various primers in specific regions (SEQ ID NOs: 40, 41, 42, 43 and 44, respectively) in the core regions of HCV subtypes 1 a, 1 b, 2 a, 2 b and 3 a and determined whether or not each of the primers enables selective isothermal amplification of the corresponding subtype.

The designing of primers according to the present invention will be illustrated by taking HCV subtype 1 a as an example. FIG. 9 shows the sequence of a region from the 5′-non-translated region (5′-NTR) to the core region of the HCV subtype 1 a RNA. The region of 318th to 676th bases (SEQ ID NO: 40) in the sequence shown in FIG. 9 is a region suitable for genotyping. It has been revealed that primers having the sites 33 and 34 as priming sites, respectively, are optimal for HCV subtype 1 a-specific isothermal amplification. Specifically, the primers corresponding to these priming sites have base sequences of SEQ ID NOs: 1 and SEQ ID NO: 2, respectively.

The sequences of subtype-specific primers for isothermal amplification determined in the same manner as above are shown in Table 1. TABLE 1 Sequence of Oligonucleotides in This Invention Gen- SEQ o- ID Sense or type NO antisense 5′-3′sequence 1a 1 Sense 5′-CACCATGAGCACGAATCCTA-3′ 2 Antisense 5′- WGCCTTGGGGATAGGCTG-3′ 1b 3 Sense 5′-CACCATGAGCACGAATCCTA-3′ 4 Antisense 5′- GAGCCATCCTGCCCACCCCA -3′ 9 Antisense 5′- GGATAGGTTGTCGCCATCCA -3′ 2a 5 Sense 5′- CCTAAACCTCAAAGAAAAACCA-3′ 6 Antisense 5′- TGGTTTTCCCCAGGATTTGCCAGT-3′ 10 Antisense 5′- CCCGTATAGGGGCCAGGGGTA -3′ 2b 21 Sense 5′- AAGTTCCCGGGYGGCGGYCAGAT-3′ 22 Antisense 5′- ARCCCTCGTTTCCGTACAGRGGCC AA-3′ 3a 7 Sense 5′- YAACATGAGCACACTTCCTA-3′ 8 Antisense 5′- TYCGCTCYGACGCGCCTTGGGGATA-3′

As shown in Table 1, the oligonucleotides of SEQ ID NOs: 1 and 2 can be used as a sense primer and an antisense primer, respectively, in the amplification of HCV subtype 1 a RNA. Likewise, the oligonucleotides of SEQ ID NOs: 3 and 4 or 9 can be used as a sense primer and an antisense primer, respectively, in the amplification of HCV subtype 1 b RNA. The oligonucleotides of SEQ ID NOs: 5 and 6 or 10 can be used as a sense primer and an antisense primer, respectively, in the amplification of HCV subtype 2 a RNA. The oligonucleotides of SEQ ID NOs: 21 and 22 can be used as a sense primer and an antisense primer, respectively, in the amplification of HCV subtype 2 b RNA. The oligonucleotides of SEQ ID NOs: 7 and 8 can be used as a sense primer and an antisense primer, respectively, in the amplification of HCV subtype 3 a RNA.

The sequences of primers for use in the present invention, however, are not limited to the above-listed sequences. It is also possible that a primer having several bases, e.g., about one to about five bases, preferably about one to three bases more or less than the above-specified sequence at the 5′-end of the corresponding primer, namely in a direction not the elongation direction of the primer, can enables isothermal amplification of the target HCV subtype 1 a. The primer herein may not contain all the bases in the sequence and may include at least eighteen consecutive bases in its 3′ end region for selective isothermal amplification of HCV subtype 1 a.

Each of the primers of the present invention may further comprise, as needed, any of other sequences in its 5′ end region, in addition to the template-specific sequence specifically hybridizing with a template represented by the sequence number. When the primer is used, for example, in NASBA (J. Compton: Nucleic acid sequence-based amplification. Nature, 1991, 350, p91-92), at least one of the pair of primers may have a T7 promoter sequence in its 5′ end region. The primers may be appropriately modified typically with a labeling material such as a radioisotope, enzyme or fluorophore, and such modified primers are also included in the primers of the present invention.

The primers of the present invention preferably each have 18 to 30 bases in a region to hybridize with a template. The base length of the primers herein does not include the length of a region which does not hybridize with a template. For example, the T7 promoter sequence region of the primer for use in NASBA is not included in the base length of 18 to 30 bases.

The primers of the present invention may further comprise one to several base substitutions (mismatches for the template) within ranges not adversely affecting the advantages of the present invention. The primers should preferably include such mismatches (base substitutions) in their 5′ end region, because base substitutions residing at the 3′ end may adversely affect the precision of genotyping.

The primers of the present invention can be used in isothermal amplification such as NASBA, but can also be used in other primer extension amplification processes such as PCR (R. K. Saiki, et al., Science, 239, 487-491 (1988)), self-sustained sequence replication (3SR) (J. C. Guatelli, et al., Proc Natl Acad Sci USA, 87, 1874-1878 (1990)), and transcription-based amplification systems (TAS) (D. Y. Kwoh, et al., Proc Natl Acad Sci USA, 86, 1173-1177 (1989)).

2. Method for Detecting HCV (HCV Genotyping)

The present invention provides a method for detecting (genotyping) HCV by isothermal amplification with the primers. FIG. 1 is a flow chart of the method for detecting or genotyping HCV according to the present invention. In this method, a virus RNA 2 is extracted from a sample 1, is mixed with a primer amplification reagent 5, is amplified by an amplification device 3 and is detected by a detection device 4. The primer amplification reagent 5 contains an amplification reagent comprising dNTPs, NTPs and a buffer solution, and a primer mixture containing a primer of SEQ ID NO: 1, 3, 5, 7 or 21 in combination with a corresponding primer of SEQ ID NOs: 2, 4, 6, 8, 9, 10 or 22. The detection can be carried out, for example, by a method in which an amplified product is subjected to electrophoresis and lengths of amplified fragments (sizes of amplification) are compared, or a method of real-time detection of an amplified product typically using fluorophore-labeled probes.

Examples of isothermal amplification techniques for use in the present invention include LAMP (T. Notomi et al., Loop-mediated isothermal amplification of DNA. Nucleic Acids Res., 28(12): e63, (2000)) and ICAN (Isothermal and Chimeric Primer-initiated Amplification of Nucleic acids; Japanese Patent No. 3433929), in addition to above-mentioned NASBA.

The method for detecting HCV according to the present invention enables simultaneous detection of two or more HCV subtypes with two or more corresponding primers for isothermal amplification.

3. Kit for the Detection (Genotyping) of HCV

The present invention provides a kit for the detection (genotyping) of HCV. The kit essentially comprises all or part of the pairs of primers of the present invention, and one or more probes for detecting HCV subtype-specific amplified products amplified with the primers.

The probe for detecting a HCV subtype-specific amplified product is labeled with an appropriate labeling material such as a radioisotope, enzyme or fluorophore and comprises a sequence complementary to a sequence including about 18 to about 30 bases on a sample HCV gene fragment which is specifically amplified by the primer of the present invention. Examples of the probe are probes having base sequences of SEQ ID NOs: 19 and 20, respectively. When used as a molecular beacon probe, the probe may be labeled with a fluorophore such as FAM or ROX at one end and with a quencher such as BHQ1 or BHQ2 at the other end.

The kit for the detection (genotyping) of HCV of the present invention essentially comprises the primers and the probes and may further comprise, as needed, any of components that can be used in gene amplification and determination of amplified products, such as molecular weight markers, enzymes, dNTPs, NTPs and sterilized water, as well as any other components.

The present invention will be illustrated in further detail with reference to several examples below, which are never intended to limit the scope of the invention.

EXAMPLE 1 Screening of Primers Capable of Typing HCV Subtype 1 a Gene by NASBA

An optimal pair of oligonucleotide primers for genotype-specific isothermal amplification by NASBA was determined by designing sense primers and antisense primers in regions in the core region of the HCV subtype 1 a gene which are capable of highly specifically typing, setting pairs of the oligonucleotide primers in various combinations and subjecting the pairs of primers to NASBA. The sense primers are oligonucleotide primers of SEQ ID NOs: 1, 24, 25, 26, 27, 28, 29, 30, 31 and 32, and the antisense primers are oligonucleotide primers of SEQ ID NOs: 11, 33, 34, 35, 36, 37, 38 and 39 listed in Table 2. Each of the antisense primer further had a sequence (AATTCTAATACGACTCACTATAGGGAGAAGG: SEQ ID NO: 45) including a T7 promoter sequence at the 5′ end. TABLE 2 SEQ Primer Sequence* location** ID NO Ref HCV1p201 5′-GAGGTCTCGTAGACCGTGCACCA-3′(23bp) 2-25bp 24 S1 HCV1p202 5′-CACCATGAGCACGAATCCTA-3′(20bp) 21-40bp 1 S2 HCV1p2O3 5′-TCAGATCGTTGGTGGAGTTTA-3′(21bp) 108-12Tbp 25 S3 HCV1p2O4 5′-TCGTTGGTGGAGTTTACTTGTT-3′(22bp) 171 -292bp 26 S4 HCV1p205 5′-AGGAAGACTTCCGAGCGGTC-3′(20bp) 172-291bp 27 S5 HCV1p206 5′-GGAAGACTTCCGAGCGGTCGCA-3′(22bp) 113-134bp 28 S6 HCV1p211 5′-CCTAAACCTCAAAGAAAAACCA-3′(22bp) 37-58bp 29 S7 HCV1p212 5′-CCAAACGTAACACCAACCGT-3′(20bp) 56-75bp 30 S8 HCV1p213 5′-AGTTCCCGGGTGGCGGTCAG-3′(20bp) 92-111bp 31 S9 HCV1p214 5′-AGACTTCCGAGCGGTCGCAAC-3′(21bp) 176-196bp 32 S10 HCV1p101 5′-AACTTGACGTCCTGTGGGCGA-3′(21bp) 75-95bp 33 A1 HCV1p102 5′-AAACTCCACCAACGATCTGA-3′(20bp) 108-127bp 34 A2 HCV1p103 5′-TGCCTTGGGGATAGGCTGGCGTCTA-3′(25bp) 204-228bp 35 A3 HCV1p104 5′-TGCCTTGGGGATAGGCTG-3′(18bp) 204-223bp 11(2) A4 HCV1p108 5′-ACGGTTGGTGTTACGTTTGG-3′(20bp) 56-75bp 36 A5 HCV1p109 5′-GGCGTCTACCTCGAGGTTGCG-3′(21bp) 191-111bp 37 A6 HCV1p112 5′-TACCTCGAGGTTGCGACCGCTCGGA-3′(25bp) 181-205bp 38 A7 HCV1p113 5′-GCCGACGTGCCTTGGGGA-3′(22bp) 218-239bp 39 A8 *:The sequences of the antisense primers A1 to A8 are exclusive of the T7 promoter sequence. **:The “Location” represents the location on SEQ ID NO: 40 where the primer is set.

FIG. 2 is a flow chart of the amplification by NASBA. NASBA can be suitably carried out with a commercially available kit, such as NUCLISENS™ Basic Kit (bioMerieux, Inc.). A solution 6 for use in the reaction contains a HCV subtype 1 a gene sample, a tested primer, reagents and other components. The solution 6 was subjected to a reaction by NASBA by holding the solution at 65° C. for 5 minutes and at 41° C. for 5 minutes; adding an enzyme 9 to the solution, followed by a reaction at 41° C. for 90 minutes in an isothermal amplification device 7. The resulting reaction product was detected with a detection device 8 by subjecting the reaction product to electrophoresis with SV1210 Cosmo-i (Hitachi High-Technologies Corporation) as the detection device 8 and determining the presence or absence of, and the position of the amplified product.

FIG. 7 shows an electropherogram of amplified products of amplification reaction using an oligonucleotide primer of SEQ ID NO: 1 as a sense primer, and those of SEQ ID NOs: 11, 33, 34, 35, 36, 37, 38 and 39 as an antisense primer, respectively. Apair of oligonucleotide primers of SEQ ID NOs: 1 and 11 was designed so as to yield, as a result of the reaction, an amplified product having a size of amplification of 217 bp. Likewise, pairs of oligonucleotide primers of SEQ ID NOs: 1 and 33, 1 and 34, 1 and 35, 1 and 36, 1 and 37, 1 and 38, and 1 and 39 were designed so as to yield amplified products having a size of amplification of 84 bp, 116 bp, 217 bp, 64 bp, 200 bp, 194 bp and 224 bp, respectively.

The product as a result of the reaction with the oligonucleotide primers of SEQ ID NOs: 1 and 33 was subjected to electrophoresis in Lane 1. Likewise, the reaction products as a result of the reactions of the oligonucleotide primers of SEQ ID NOs: 1 and 34, 1 and 35, 1 and 11, 1 and 36, 1 and 37, 1 and 38, and 1 and 39 were subjected to electrophoreses in Lanes 2, 3, 4, 5, 6, 7 and 8, respectively.

Amplified products 21 and 22 were detected at a base length of 317 bp and a base length of 78 bp, respectively, in Lane 1. Specifically, a non-specific amplified product was detected at another portion than at 78 bp which is in the vicinity of the set base length, 84 bp. An amplified product 23 was detected at a base length of 116 bp in Lane 2. An amplified product 24 was detected at a base length of 217 bp in Lane 3. An amplified product 25 was detected at a base length of 217 bp in Lane 4. An amplified product 26 was detected at a base length of 64 bp in Lane 5. In Lane 6, an amplified product 27 was detected at a base length of 51 bp. Namely, no amplified product was detected at a designed base length of 200 bp. In Lane 7, amplified products 28 and 29 were detected at a base length of 167 bp and a base length of 210 bp, respectively. Specifically, no amplified product was detected at the designed base length of 194 bp, but non-specific amplified products were detected at other positions. An amplified product 30 was detected at a base length of 224 bp in Lane 8.

These results show that the pairs of oligonucleotide primers corresponding to SEQ ID NOs: 1 and 33, 1 and 37, and 1 and 38 yielded non-specific amplified products (Lanes 1, 6 and 7), but the pairs of oligonucleotide primers corresponding to SEQ ID NOs: 1 and 34, 1 and 35, 1 and 36, 1 and 39, and 1 and 11 yielded specific amplified products to the HCV subtype 1 a (Lanes 2, 3, 4, 5 and 8).

Next, the pairs of oligonucleotide primers corresponding to SEQ ID NOs: 1 and 34, 1 and 35, 1 and 36, 1 and 39, and 1 and 11, respectively, were subjected to determination of amplified products by NASBA using a HCV subtype 1 b sample. This test was carried out to determine whether or not these oligonucleotide primers yield amplification specific only to the HCV subtype 1 a gene, since they were designed so as to genotype the HCV subtype 1 a gene and not to yield amplified products in the other subtypes.

FIG. 8 shows an electropherogram of amplified products of amplification reaction of the HCV subtype 1 b sample with the oligonucleotide primer of SEQ ID NO: 1 as a sense primer, and those of SEQ ID NOs: 11 and 39 as an antisense primer, respectively. The reaction products as a result of amplification of the subtype 1 b sample with the pair of oligonucleotide primers corresponding to SEQ ID NOs: 1 and 11, and with the pair of oligonucleotide primers corresponding to SEQ ID NOs: 1 and 39 were subjected to electrophoresis in Lanes 1 and 2, respectively.

An amplified product 31 was detected at a base length of 100 bp in Lane 1. Namely, this pair of oligonucleotide primers yielded no amplified product in the case of the HCV subtype 1 b sample at the designed base length of 217 bp, demonstrating that this pair specifically amplifies the HCV subtype 1 a gene alone. An amplified product 32 was detected at a base length of 219 bp in Lane 2. This position of the amplified product is different from that of the HCV subtype 1 a sample, at a base length of 224 bp, only by 5 bp, showing that this pair of oligonucleotide primers does not enable genotyping based on the base length of the amplified product. In contrast, the pair of oligonucleotide primers corresponding to SEQ ID NOs: 1 and 11 enables genotyping between the HCV subtype 1 a and HCV subtype 1 b genes based on the base length of the amplified product.

In the same way as above, whether or not amplified products by NASBA were detected at estimated base lengths was determined in samples of the other HCV subtypes, to find that the pair of oligonucleotide primers corresponding to SEQ ID NOs: 1 and 11 yields amplification specific to the HCV subtype 1 a. The results are shown in Table 3. TABLE 3 Size of Amplification and Assessment Size (bp) of Base length(bp) of amplicon the region sandwiched Sense Antisense NASBA between the primers Assessment* S1 A1 100 91 x A2 134 125 x A3 235 226 x A4 235 226 x A5 82 73 x A6 218 209 x S2 A1 84 75 x A2 116 107 Δ A3 217 208 Δ A4 217 208 ∘ A5 64 55 Δ A6 200 191 x A7 194 185 x A8 224 215 Δ S3 A3 130 121 x A4 130 121 x A6 113 104 x A7 107 98 x A8 137 128 Δ S4 A3 125 116 x A4 125 116 x A6 108 99 x S5 A3 66 57 x A4 66 57 x S6 A3 65 56 x A4 65 56 x S7 A1 68 59 x A2 100 91 x A3 201 192 x A4 201 192 Δ A6 184 175 x A7 178 169 x A8 208 199 x S8 A2 81 72 x A3 183 174 x A4 183 174 x A6 165 156 x S9 A3 62 53 x A4 146 137 x A6 129 120 x A7 121 112 x A8 151 142 x S10 A3 62 53 x A4 62 53 x A8 67 58 Δ *Criteria for Assessment: Good(∘): Primer capable of genotyping Fair(Δ): Primer capable of amplifying but incapable of genotyping Failure(x): Primer incapable of amplifying

Table 3 shows that the pair of oligonucleotide primers corresponding to SEQ ID NOs: 1 and 11 is suitable for the genotyping of the HCV subtype 1 a gene. The sense primer corresponding to SEQ ID NO: 1 is considered to be capable of isothermally amplifying the HCV subtype 1 a even if the priming site is narrowed by about two bases or less, or extended by about five bases or less at the 5′ end and to be capable of genotyping the HCV subtype 1 a even if the priming site is narrowed by about one or two bases at the 5′ end. The antisense primer corresponding to SEQ ID NO: 11 is considered to be capable of isothermally amplifying the HCV subtype 1 a even if the priming site is extended by about twelve bases or less at the 5′ end and to be capable of genotyping the HCV subtype 1 a even if the priming site is extended by about five bases or less at the 5′ end.

EXAMPLE 2 Screening of Primers Capable of Genotyping HCV Subtypes 1 b, 2 a, 2 b and 3 a

Optimal pairs of oligonucleotide primers for genotype-specific isothermal amplification of HCV subtypes 1 b, 2 a, 2 b and 3 a genes by NASBA were determined by the procedure of Example 1.

(1) HCV Subtype 1 b Gene

Primers listed in Table 4 were designed based on the sequence of a specific region capable of typing the core region of the HCV subtype 1 b gene (SEQ ID NO: 41 corresponding to 1 to 325 bp of the core region of HCV subtype 1 b). Different pairs of these primers were subjected to isothermal amplification by NASBA under the same conditions as in Example 1 using, as a template, a HCV subtype 1 b gene sample, and the presence or absence of, and the position of amplified product were determined by electrophoresis. In addition, the presence or absence of, and the position of amplified product by NASBA using samples of the other HCV subtypes were determined on pairs of primers which yielded the amplified product so as to determine whether or not the pairs of primers are capable of genotyping the HCV subtype 1 b gene. The set primer regions and results are shown in Table 4. TABLE 4 Position on Primer SEQ ID NO: 41* Assessment** Remarks HCV2p201 21-40 bp ∘ Corresponding to SEQ ID Nos: 3 and 17 HCV2p202 37-58 bp Δ HCV2p203 92-111 bp x HCV2p204 108-127 bp x HCV2p205 192-219 bp x HCV2p101 191-214 bp Δ HCV2p102 201-220 bp ∘ Corresponding to SEQ ID No: 9 HCV2p103 242-260 bp x HCV2p104 296-305 bp ∘ Corresponding to SEQ ID Nos: 4 and 12 *The position represents the position of set primer on SEQ ID NO: 41 **Criteria for Assessment: Good(∘): Primer capable of genotyping Fair(Δ): Primer capable of amplifying but incapable of genotyping Failure(x): Primer incapable of amplifying

Table 4 shows that the oligonucleotide primers corresponding to SEQ ID NOs: 3, 4 and 9 are suitable for the genotyping of the HCV subtype 1 b gene. The sense primer corresponding to SEQ ID NO: 3 is considered to be capable of isothermally amplifying the HCV subtype 1 b gene even if the priming site is narrowed by about two bases or less, or extended by about five bases or less at the 5′ end and to be capable of genotyping the HCV subtype 1 b gene even if the priming site is narrowed by about one or two bases at the 5′ end. The antisense primer corresponding to SEQ ID NO: 4 or 9 is considered to be capable of isothermally amplifying the HCV subtype 1 b gene even if the priming site is extended by about ten bases or less at the 5′ end and to be capable of genotyping the HCV subtype 1 b gene even if the priming site is extended by about six bases or less at the 5′ end. P (2) HCV Subtype 2 a Gene

Primers listed in Table 5 were designed based on the sequence of a specific region capable of typing the core region of the HCV subtype 2 a gene (SEQ ID NO: 42 corresponding to 21 to 295 bp of the core region of HCV subtype 2 a). Different pairs of these primers were subjected to isothermal amplification by NASBA under the same conditions as in Example 1 using, as a template, a HCV subtype 2 a gene sample, and the presence or absence of, and the position of amplified product were determined by electrophoresis. In addition, the presence or absence of, and the position of amplified product by NASBA using samples of the other HCV subtypes were determined on pairs of primers which yielded the amplified product so as to determine whether or not the pairs of primers are capable of genotyping the HCV subtype 2 a gene. The set primer regions and results are shown in Table 5. TABLE 5 Position on Primer SEQ ID NO: 42* Assessment** Remarks HCV3p201 21-40 bp x HCV3p202 37-58 bp ∘ Corresponding to SEQ ID Nos: 5 and 18 HCV3p203 41-63 bp x HCV3p204 55-78 bp x HCV3p205 88-106 bp x HCV3p206 151-175 bp x HCV3p207 151-174 bp x HCV3p101 202-227 bp x HCV3p102 217-240 bp ∘ Corresponding to SEQ ID Nos: 6 and 13 HCV3p103 242-260 bp ∘ Corresponding to SEQ ID No: 10 *The position represents the position of set primer on SEQ ID NO: 42 **Criteria for Assessment: Good(∘): Primer capable of genotyping Fair(Δ): Primer capable of amplifying but incapable of genotyping Failure(x): Primer incapable of amplifying

Table 5 shows that the oligonucleotide primers corresponding to SEQ ID NOs: 5, 6 and 10 are suitable for the genotyping of the HCV subtype 2 a gene. The sense primer corresponding to SEQ ID NO: 5 is considered to be capable of isothermally amplifying and genotyping the HCV subtype 2 a gene even if the priming site is narrowed by about four bases or less, or extended by about three bases or less at the 5′ end. The antisense primer corresponding to SEQ ID NO: 6 or 10 is considered to be capable of isothermally amplifying the HCV subtype 2 a gene even if the priming site is narrowed by about four bases or less, or extended by about eight bases or less at the 5′ end and to be capable of genotyping the HCV subtype 2 a gene even if the priming site is narrowed by about four bases or less or extended by about one base or less at the 5′ end.

(3) HCV Subtype 2 b Gene

Primers listed in Table 6 were designed based on the sequence of a specific region capable of typing the core region of the HCV subtype 2 b gene (SEQ ID NO: 43 corresponding to 1 to 305 bp of the core region of HCV subtype 2 b). Different pairs of these primers were subjected to isothermal amplification by NASBA under the same conditions as in Example 1 using, as a template, a HCV subtype 2 b gene sample, and the presence or absence of, and the position of amplified product were determined by electrophoresis. In addition, the presence or absence of, and the position of amplified product by NASBA using samples of the other HCV subtypes were determined on pairs of primers which yielded the amplified product so as to determine whether or not the pairs of primers are capable of genotyping the HCV subtype 2 b gene. The set primer regions and results are shown in Table 6. TABLE 6 Position on Primer SEQ ID NO: 43* Assessment** Remarks HCV4p201 16-40 bp x HCV4p202 37-58 bp Δ HCV4p203 21-40 bp x HCV4p204 91-113 bp ∘ Corresponding to SEQ ID Nos: 21 and 23 HCV4p205 92-110 bp Δ HCV4p206 108-132 bp Δ HCV4p101 210-235 bp Δ HCV4p102 241-257 bp Δ HCV4p103 244-264 bp x HCV4p104 270-295 bp ∘ Corresponding to SEQ ID No: 22 *The position represents the position of set primer on SEQ ID NO: 43 **Criteria for Assessment: Good(∘): Primer capable of genotyping Fair(Δ): Primer capable of amplifying but incapable of genotyping Failure(x): Primer incapable of amplifying

Table 6 shows that the oligonucleotide primers corresponding to SEQ ID NOs: 21 and 22 are suitable for the genotyping of the HCV subtype 2 b gene. The sense primer corresponding to SEQ ID NO: 21 is considered to be capable of isothermally amplifying the HCV subtype 2 b gene even if the priming site is narrowed by about two bases or less, or extended by about seventeen bases or less at the 5′ end and to be capable of genotyping the HCV subtype 2 b gene even if the priming site is narrowed by about two bases or less at the 5′ end. The antisense primer corresponding to SEQ ID NO: 22 is considered to be capable of isothermally amplifying the HCV subtype 2 b gene even if the priming site is narrowed by about five bases or less at the 5′ end and to be capable of genotyping the HCV subtype 2 b gene even if the priming site is narrowed by about five bases or less at the 5′ end.

(4) HCV Subtype 3 a Gene

Primers listed in Table 7 were designed based on the sequence of a specific region capable of typing the core region of the HCV subtype 3 a gene (SEQ ID NO: 44 corresponding to 1 to 366 bp of the core region of HCV subtype 3 a). Pairs of these primers were subjected to isothermal amplification by NASBA under the same conditions as in Example 1 using, as a template, a HCV subtype 3 a gene sample, and the presence or absence of, and the position of amplified product were determined by electrophoresis. In addition, the presence or absence of, and the position of amplified product by NASBA using samples of the other HCV subtypes were determined on pairs of primers which yielded the amplified product so as to determine whether or not the pairs of primers are capable of genotyping the HCV subtype 3 a gene. The set primer regions and results are shown in Table 7. TABLE 7 Position on Primer SEQ ID NO: 44* Assessment** Remarks HCV5p201 21-40 bp ∘ Corresponding to SEQ ID No: 7 HCV5p202 37-58 bp Δ HCV5p203 61-81 bp x HCV5p204 91-111 bp x HCV5p205 109-133 bp Δ HCV5p206 171-195 bp x HCV5p101 216-240 bp ∘ Corresponding to SEQ ID Nos: 8 and 14 HCV5p102 227-245 bp Δ HCV5p103 244-267 bp Δ HCV5p104 270-288 bp x HCV5p105 285-304 bp Δ HCV5p106 340-356 bp x *The position represents the position of set primer on SEQ ID NO: 44 **Criteria for Assessment: Good(∘): Primer capable of genotyping Fair(Δ): Primer capable of amplifying but incapable of genotyping Failure(x): Primer incapable of amplifying

Table 7 shows that the oligonucleotide primers corresponding to SEQ ID NOs: 7 and 8 are suitable for the genotyping of the HCV subtype 3 a gene. The sense primer corresponding to SEQ ID NO: 7 is considered to be capable of isothermally amplifying the HCV subtype 3 a gene even if the priming site is narrowed by about two bases or less, or extended by about five bases or less at the 5′ end and to be capable of genotyping the HCV subtype 3 a gene even if the priming site is narrowed by about two bases or less at the 5′ end. The antisense primer corresponding to SEQ ID NO: 8 is considered to be capable of isothermally amplifying and genotyping the HCV subtype 3 a gene even if the priming site is narrowed by about five bases or less at the 5′ end.

EXAMPLE 3 Genotyping of HCV Subtypes 1 a, 1 b, 2 a, 2 b and 3 a Genes by NASBA

Genotyping of HCV was carried out by isothermal amplification according to NASBA and electrophoresis by the procedure of Example 1. More specifically, the sense primers used are oligonucleotide primers corresponding to SEQ ID NOs: 1, 3, 5 and 7, and the antisense primers are oligonucleotide primers corresponding to SEQ ID NOs: 11, 12, 13 and 14 each further having a sequence including a T7 promoter sequence at the 5′ end.

A pair of oligonucleotide primers corresponding to SEQ ID NOs: 1 and 2 was so designed as to yield an amplified product having a size of 217 bp as a result of the amplification of a sample HCV subtype 1 a RNA. Likewise, a pair of oligonucleotide primers corresponding to SEQ ID NOs: 3 and 4, a pair of oligonucleotide primers corresponding to SEQ ID NOs: 5 and 6, and a pair of oligonucleotide primers corresponding to SEQ ID NOs: 7 and 8 were so designed as to yield amplified products having sizes of 209 bp, 234 bp and 229 bp as a result of the amplification of HCV subtype 1 b RNA sample, HCV subtype 2 a RNA sample, and HCV subtype 3 a RNA sample respectively.

FIG. 3 shows the resulting electropherogram. Amplified products 10, 11, 12 and 13 in Lanes 1, 2, 3 and 4 as a result of amplification of the HCV subtypes 1 a, 1 b, 2 a and 3 a RNA samples were detected at base lengths of 217 bp, 304 bp, 234 bp and 229 bp, respectively. In other words, the samples of HCV subtypes 1 a, 1 b, 2 a and 3 a RNAs yield amplified products having different sizes of amplification of 217 bp, 304 bp, 234 bp and 229 bp, respectively, with the oligonucleotide primers capable of carrying out genotype-specifically amplification.

These results show that the amplified product as a result of isothermal amplification of the HCV subtype 1 a RNA with the pair of oligonucleotide primers corresponding to SEQ ID NOs: 1 and 2 is positioned at the estimated length of the amplified gene, and that those of the other HCV subtypes 1 b, 2 a and 3 a samples were positioned at the estimated lengths of the amplified genes. Namely, it is verified that the oligonucleotide primers according to the present invention are capable of genotyping of HCV subtypes.

EXAMPLE 4 Real-Time Detection of HCV Subtypes 1 b and 2 a Genes by NASBA with Molecular Beacon

HCV subtypes 1 b and 2 a, which invite many infections in Japan, were genotyped with a real-time detection device. For selective real-time detection, oligonucleotide primers corresponding to SEQ ID NOs: 15 and 16, which correspond to oligonucleotide primers of SEQ ID NOs: 9 and 10, except with a Tag sequence added at the 5′ end, were used as antisense primers, and oligonucleotide primers corresponding to SEQ ID NO: 17 and 18, which correspond to oligonucleotide primers of SEQ ID NOs: 3 and 5, except with a T7 promoter added at the 5′ end, were used as sense primers.

Molecular beacon probes (S. Tyagi, et al., Nature Biotechnol, 14, 303-308(1996)) were used as a probe in the real-time detection. The molecular beacon probes were designed so as to have a Tag sequence and base sequences corresponding to SEQ ID NOs: 19 and 20, respectively, for distinguishing the Tag sequence. The molecular beacon corresponding to SEQ ID NO: 19 was modified with FAM as a fluorophore and with BHQ1 as a quencher. The molecular beacon corresponding to SEQ ID NO: 20 was modified with ROX as a fluorophore and with BHQ2 as a quencher.

The sample HCV gene was amplified by NASBA by the procedure of Example 1, except for using NUCLISENS™ Basic Kit (bioMerieux, Inc.).

FIG. 4 is a flow chart of real-time detection (genotyping) of the HCV gene. Specifically, a solution 14 containing, for example, a sample, primers and reagents was mixed with an enzyme 16, was subjected to amplification, and the amplified product was detected in real-time in an isothermal amplification/detection device 15. The isothermal amplification/detection device 15 used herein was Mx 3000p (Stratagene). The results are shown in FIGS. 5A and 5B. FIGS. 5A and 5B show results 17 and 18 in which a HCV subtype 1 b gene RNA and a HCV subtype 2 a gene RNA as samples were amplified, respectively, with the ordinate indicating the fluorescent intensity and the abscissa indicating the time. In the figures, the fluorescent intensity of FAM capable of identifying the HCV subtype 1 b amplified product is indicated by solid lines, and the fluorescent intensity of ROX capable of identifying the HCV subtype 2 a amplified product is indicated by dashed lines. FIG. 5A shows that only the fluorescent intensity of FAM increases with time, indicating that the sample is of the HCV subtype 1 b. In contrast, FIG. 5B shows that only the fluorescence intensity of ROX increases with time, indicating that the sample herein is of the HCV subtype 2 a. These results show that the oligonucleotide primers of the present invention do not interfere with amplification with another primer and are sufficiently accurately usable in the amplification, that they can easily genotype HCV subtypes based on the kind of fluorophore and can quantitatively determine the HCV subtypes by measuring the rise time of fluorescent intensity.

EXAMPLE 5 Simultaneous Detection of HCV Subtypes 1 b and 2 b by NASBA

HCV genotyping was carried out using oligonucleotide primers corresponding to SEQ ID NOs: 3 and 21 as sense primers, and oligonucleotide primers corresponding to SEQ ID NOs: 12 and 23 as antisense primers. The antisense primers correspond to SEQ ID NOs: 4 and 22, except for further having a T7 promoter sequence at the 5′ end.

FIG. 6 shows the resulting electropherogram. The oligonucleotide primers corresponding to SEQ ID NOs: 3 and 12 were so designed as to yield an amplified product having a size of amplification of 209 bp as a result of the amplification of the HCV subtype 1 b RNA. The oligonucleotide primers corresponding to SEQ ID NOs: 21 and 23 were so designed as to yield an amplified product having a size of 214 bp as a result of the amplification of the HCV subtype 2 b RNA.

The results of the amplification reaction with the oligonucleotide primers corresponding to SEQ ID NOs: 3 and 12 are shown in Lanes 1 and 2. The results of the amplification reaction using with oligonucleotide primers corresponding to SEQ ID NOs: 21 and 23 are shown in Lanes 3 and 4. An amplified product 19 was detected at a base length of 209 bp in Lane 1 as a result of the amplification of the HCV subtype 1 b RNA as a sample. In contrast, no amplified product was detected in Lane 2 as a result of the amplification of the HCV subtype 2 b as a sample. An amplified product 20 was detected at a base length of 214 bp in Lane 4 as a result of the amplification of the HCV subtype 2 b RNA as a sample. In contrast, no amplified product was detected in Lane 3 as a result of the amplification of the HCV subtype 1 b as a sample. These results show that the oligonucleotide primers of the present invention yield amplified products at estimated base lengths only when reacted with samples having corresponding genotypes.

The oligonucleotide primers of the present invention are usable in the detection and genotyping of hepatitis C virus and can thereby be widely used in researches on HCV, such as studies on pathoses, estimation and determination of efficacies of agents depending on the subtypes of HCV.

While the present invention has been described with reference to what are presently considered to be the preferred embodiments, it is to be understood that the invention is not limited to the disclosed embodiments. On the contrary, the invention is intended to cover various modifications and equivalent arrangements included within the spirit and scope of the appended claims. The scope of the following claims is to be accorded the broadest interpretation so as to encompass all such modifications and equivalent structures and functions.

Sequence Listing Free Text

SEQ ID NO: 1—Description of Artificial Sequence: sense primer for the amplification of HCV subtype 1 a

SEQ ID NO: 2—Description of Artificial Sequence: antisense primer for the amplification of HCV subtype 1 a

SEQ ID NO: 3—Description of Artificial Sequence: sense primer for the amplification of HCV subtype 1 b

SEQ ID NO: 4—Description of Artificial Sequence: antisense primer for the amplification of HCV subtype 1 b

SEQ ID NO: 5—Description of Artificial Sequence: sense primer for the amplification of HCV subtype 2 a

SEQ ID NO: 6—Description of Artificial Sequence: antisense primer for the amplification of HCV subtype 2 a

SEQ ID NO: 7—Description of Artificial Sequence: sense primer for the amplification of HCV subtype 3 a

SEQ ID NO: 8—Description of Artificial Sequence: antisense primer for the amplification of HCV subtype 3 a

SEQ ID NO: 9—Description of Artificial Sequence: antisense primer for the amplification of HCV subtype 1 b

SEQ ID NO: 10—Description of Artificial Sequence: antisense primer for the amplification of HCV subtype 2 a

SEQ ID NO: 11—Description of Artificial Sequence: antisense primer with T7 promoter sequence for the amplification of HCV subtype 1 a

SEQ ID NO: 12—Description of Artificial Sequence: antisense primer with T7 promoter sequence for the amplification of HCV subtype 1 b

SEQ ID NO: 13—Description of Artificial Sequence: antisense primer with T7 promoter sequence for the amplification of HCV subtype 2 a

SEQ ID NO: 14—Description of Artificial Sequence: antisense primer with T7 promoter sequence for the amplification of HCV subtype 3 a

SEQ ID NO: 15—Description of Artificial Sequence: antisense primer with Tag sequence for the amplification of HCV subtype 1 b

SEQ ID NO: 16—Description of Artificial Sequence: antisense primer with Tag sequence for the amplification of HCV subtype 2 a

SEQ ID NO: 17—Description of Artificial Sequence: sense primer with T7 promoter sequence for the amplification of HCV subtype 1 b

SEQ ID NO: 18—Description of Artificial Sequence: sense primer with T7 promoter sequence for the amplification of HCV subtype 2 a

SEQ ID NO: 19—Description of Artificial Sequence: molecular beacon sequence with Tag sequence

SEQ ID NO: 20—Description of Artificial Sequence: molecular beacon sequence with Tag sequence

SEQ ID NO: 21—Description of Artificial Sequence: sense primer for the amplification of HCV subtype 2 b

SEQ ID NO: 22—Description of Artificial Sequence: antisense primer for the amplification of HCV subtype 2 b

SEQ ID NO: 23—Description of Artificial Sequence: antisense primer with T7 promoter sequence for the amplification of HCV subtype 2 b

SEQ ID NO: 24—Description of Artificial Sequence: HCV subtype 1 a sense primer

SEQ ID NO: 25—Description of Artificial Sequence: HCV subtype 1 a sense primer

SEQ ID NO: 26—Description of Artificial Sequence: HCV subtype 1 a sense primer

SEQ ID NO: 27—Description of Artificial Sequence: HCV subtype 1 a sense primer

SEQ ID NO: 28—Description of Artificial Sequence: HCV subtype 1 a sense primer

SEQ ID NO: 29—Description of Artificial Sequence: HCV subtype 1 a sense primer

SEQ ID NO: 30—Description of Artificial Sequence: HCV subtype 1 a sense primer

SEQ ID NO: 31—Description of Artificial Sequence: HCV subtype 1 a sense primer

SEQ ID NO: 32—Description of Artificial Sequence: HCV subtype 1 a sense primer

SEQ ID NO: 33—Description of Artificial Sequence: HCV subtype 1 a antisense primer with T7 promoter sequence

SEQ ID NO: 34—Description of Artificial Sequence: HCV subtype 1 a antisense primer with T7 promoter sequence

SEQ ID NO: 35—Description of Artificial Sequence: HCV subtype 1 a antisense primer with T7 promoter sequence

SEQ ID NO: 36—Description of Artificial Sequence: HCV subtype 1 a antisense primer with T7 promoter sequence

SEQ ID NO: 37—Description of Artificial Sequence: HCV subtype 1 a antisense primer with T7 promoter sequence

SEQ ID NO: 38—Description of Artificial Sequence: HCV subtype 1 a antisense primer with T7 promoter sequence

SEQ ID NO: 39—Description of Artificial Sequence: HCV subtype 1 a antisense primer with T7 promoter sequence

SEQ ID NO: 40—HCV subtype 1 a-specific core region

SEQ ID NO: 41—HCV subtype 1 b-specific core region

SEQ ID NO: 42—HCV subtype 2 a-specific core region

SEQ ID NO: 43—HCV subtype 2 b-specific core region

SEQ ID NO: 44—HCV subtype 3 a-specific core region

SEQ ID NO: 45—Description of Artificial Sequence: sequence with T7 promoter sequence 

1. A primer set for isothermal amplification of hepatitis C virus containing at least one pair of primers each of which comprises at least eighteen consecutive bases corresponding to a 3′ end region of one base sequence selected from the group consisting of SEQ ID NOs: 1-10, 21 and
 22. 2. The primer set according to claim 1, wherein at least one of the pair of primers further comprises a T7 promoter sequence.
 3. The primer set according to claim 1 containing at least one pair of primes selected from the following (1) to (5): (1) a pair of primers comprising at least eighteen consecutive bases corresponding to a 3′ end region of the base sequences of SEQ ID NOs: 1 and 2, respectively; (2) a pair of primers comprising at least eighteen consecutive bases corresponding to a 3′ end region of the base sequences of SEQ ID NOs: 3 and 4, respectively, or a pair of primers comprising at least eighteen consecutive bases corresponding to a 3′ end region of the base sequences of SEQ ID NOs: 3 and 9, respectively; (3) a pair of primers comprising at least eighteen consecutive bases corresponding to a 3′ end region of the base sequences of SEQ ID NOs: 5 and 6, respectively, or a pair of primers comprising at least eighteen consecutive bases corresponding to a 3′ end region of the base sequences of SEQ ID NOs: 5 and 10, respectively; (4) a pair of primers comprising at least eighteen consecutive bases corresponding to a 3′ end region of the base sequences of SEQ ID NOs: 7 and 8, respectively; and (5) a pair of primers comprising at least eighteen consecutive bases corresponding to a 3′ end region of the base sequences of SEQ ID NOs: 21 and 22, respectively.
 4. The primer set according to claim 3, wherein at least one of the pair of primers further comprises a T7 promoter sequence.
 5. A method for detecting hepatitis C virus, comprising the steps of: subjecting a clinical sample to isothermal amplification with at least one pair of primers selected from the following pairs of primers (1) to (5); and determining a subtype of hepatitis C virus based on the resulting amplified product: (1) a pair of primers comprising at least eighteen consecutive bases corresponding to a 3′ end region of the base sequences of SEQ ID NOs: 1 and 2, respectively; (2) a pair of primers comprising at least eighteen consecutive bases corresponding to a 3′ end region of the base sequences of SEQ ID NOs: 3 and 4, respectively, or a pair of primers comprising at least eighteen consecutive bases corresponding to a 3′ end region of the base sequences of SEQ ID NOs: 3 and 9, respectively; (3) a pair of primers comprising at least eighteen consecutive bases corresponding to a 3′ end region of the base sequences of SEQ ID NOs: 5 and 6, respectively, or a pair of primers comprising at least eighteen consecutive bases corresponding to a 3′ end region of the base sequences of SEQ ID NOs: 5 and 10, respectively; (4) a pair of primers comprising at least eighteen consecutive bases corresponding to a 3′ end region of the base sequences of SEQ ID NOs: 7 and 8, respectively; and (5) a pair of primers comprising at least eighteen consecutive bases corresponding to a 3′ end region of the base sequences of SEQ ID NOs: 21 and 22, respectively.
 6. The method according to claim 5, wherein at least one of the pair of primers further comprises a T7 promoter sequence.
 7. The method according to claim 5, further comprising simultaneously determining two or more subtypes of hepatitis C virus with two or more pairs of primers.
 8. A kit for detecting hepatitis C virus, comprising at least one pair of primers selected from the following pairs of primers (1) to (5); and at least one probe containing a sequence complementary to an amplified product amplified by the action of the at least one pair of primers and serving to detect the amplified product: (1) a pair of primers comprising at least eighteen consecutive bases corresponding to a 3′ end region of the base sequences of SEQ ID NOs: 1 and 2, respectively; (2) a pair of primers comprising at least eighteen consecutive bases corresponding to a 3′ end region of the base sequences of SEQ ID NOs: 3 and 4, respectively, or a pair of primers comprising at least eighteen consecutive bases corresponding to a 3′ end region of the base sequences of SEQ ID NOs: 3 and 9, respectively; (3) a pair of primers comprising at least eighteen consecutive bases corresponding to a 3′ end region of the base sequences of SEQ ID NOs: 5 and 6, respectively, or a pair of primers comprising at least eighteen consecutive bases corresponding to a 3′ end region of the base sequences of SEQ ID NOs: 5 and 10, respectively; (4) a pair of primers comprising at least eighteen consecutive bases corresponding to a 3′ end region of the base sequences of SEQ ID NOs: 7 and 8, respectively; and (5) a pair of primers comprising at least eighteen consecutive bases corresponding to a 3′ end region of the base sequences of SEQ ID NOs: 21 and 22, respectively.
 9. The kit according to claim 8, wherein at least one of the at least one pair of primers further comprises a T7 promoter sequence. 